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diff FastQC/rgFastQC.xml @ 9:c13fa2748191 draft

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author fubar
date Mon, 03 Jun 2013 23:25:42 -0400
parents 42251cbdeeac
children
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--- a/FastQC/rgFastQC.xml	Mon Jun 03 23:11:58 2013 -0400
+++ b/FastQC/rgFastQC.xml	Mon Jun 03 23:25:42 2013 -0400
@@ -1,13 +1,13 @@
 <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53">
   <description>reporting for short read sequence</description>
   <command interpreter="python">
-    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_INSTALL_PATH/fastqc"
+    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_BINARY_PATH"
 #if $contaminants.dataset and str($contaminants) > ''
 -c "$contaminants"
 #end if
   </command>
   <requirements>
-    <requirement type="set_environment">FASTQC_INSTALL_PATH</requirement>
+    <requirement type="set_environment">FASTQC_BINARY_PATH</requirement>
     <requirement type="package" version="0.10.1">FastQC</requirement>
   </requirements>
   <inputs>